Aims: This study compares the WHO (2007) and the National Health Examination Survey (NHANES III) reference intervals and investigates the differences when applied on a Canadian cohort of older children and adolescents. Methods: We calculated height, weight and BMI z-scores of 4375 consecutive patients (1993 female, 45.6%) aged 5 - 20 years attending outpatient clinics at a single tertiary care centre using reference data of the latest NHANES (III) survey and the WHO (2007) growth charts. To address age dependency, data was stratified into age groups. Results: Using the NHANES III reference intervals, medians of weight (+0.46), height (+0.29) and BMI z-scores (+0.46) were significantly non-zero. The WHO (2007) growth charts yielded medians of +2.05, +0.32, +0.53 for weight, height and BMI z-scores respectively, all significantly non-zero. When comparing both growth charts, Canadian children had significantly different weight and BMI z-scores (p < 0.0001) with WHO growth charts whereas height z-score did not differ. Obesity rates (BMI z-score > 95th percentile) doubled from 8.6% to 16.0%. A significant age dependency was observed with higher WHO (2007) weight z-scores (>7 years) and higher BMI z-scores (7 to 13 years) and no significant difference was observed for height z-scores across all age groups. Gender differences were observed for weight z-scores (>9 years) and BMI (males: 9 - 11 years, p = 0.0118; 11 - 13 years, p = 0.0069) whereas no significant difference was found in height z-scores across all age groups. Conclusion: Our results reveal substantial differences between both reference populations and thus interpretation needs be done with caution, especially when labelling results as abnormal.